Abstract
An algorithm for retention time alignment of mass shifted hydrogen-deuterium exchange (HDX) data based on an iterative distance minimization procedure is described. The algorithm performs pairwise comparisons in an iterative fashion between a list of features from a reference file and a file to be time aligned to calculate a retention time mapping function. Features are characterized by their charge, retention time and mass of the monoisotopic peak. The algorithm is able to align datasets with mass shifted features, which is a prerequisite for aligning hydrogen-deuterium exchange mass spectrometry datasets. Confidence assignments from the fully automated processing of a commercial HDX software package are shown to benefit significantly from retention time alignment prior to extraction of deuterium incorporation values.
References
Zhang, Z.M., Chen, S., Liang, Y.Z.: Peak alignment using wavelet pattern matching and differential evolution. Talanta 83, 1108–1117 (2011)
Tomasi, G., van der Berg, F., Andersson, C.: Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data. J. Chemometr. 18, 231–241 (2004)
Ahmad, I., Suits, F., Hoekman, B., Swertz, M.A., Byelas, H., Dijkstra, M., Hooft, R., Katsubo, D., van Breukelen, B., Bischoff, R., Horvatovich, P.: A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data. Bioinformatics 27, 1176–1178 (2011)
Hoffmann, N., Stoye, J.: ChromA: Signal-based retention time alignment for chromatography-mass spectrometry data. Bioinformatics 25, 2080–2081 (2009)
Lommen, A.: MetAlign: Interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal. Chem. 81, 3079–3086 (2009)
Wang, S.Y., Ho, T.J., Kuo, C.H., Tseng, Y.J.: Chromaligner: A web server for chromatogram alignment. Bioinformatics 26, 2338–2339 (2010)
Konermann, L., Pan, J., Liu, Y.H.: Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem. Soc. Rev. 40, 1224–1234 (2011)
Center, S.P.: Software:ReAdW. (2012); Available at: http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW#Current_Version. Accessed September 3, 2012
Bellew, M., Coram, M., Fitzgibbon, M., Igra, M., Randolph, T., Wang, P., May, D., Eng, J., Fang, R., Lin, C., Chen, J., Goodlett, D., Whiteaker, J., Paulovich, A., McIntosh, M.: A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 22, 1902–1909 (2006)
Chik, J.K., Graaf, J.L.V., Schriemer, D.C.: Quantitating the statistical distribution of deuterium incorporation to extend the utility of H/D exchange MS data. Anal. Chem. 78, 207–214 (2006)
Chalmers, M.J., Busby, S.A., Pascal, B.D., He, Y., Hendrickson, C.L., Marshall, A.G., Griffin, P.R.: Probing protein ligand interactions by automated hydrogen/deuterium exchange mass spectrometry. Anal. Chem. 78, 1005–1014 (2006)
Author information
Authors and Affiliations
Corresponding author
Additional information
John D. Venable and William Scuba contributed equally to this work.
All work completed at GNF.
Rights and permissions
About this article
Cite this article
Venable, J.D., Scuba, W. & Brock, A. Feature Based Retention Time Alignment for Improved HDX MS Analysis. J. Am. Soc. Mass Spectrom. 24, 642–645 (2013). https://doi.org/10.1007/s13361-012-0566-9
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13361-012-0566-9